Re: [ccp4bb] am I doing this right?

2021-10-13 Thread Andrew Leslie - MRC LMB
Hi Ian, James, I have a strong feeling that I have seen this result before, and it was due to Andy Hammersley at ESRF. I’ve done a literature search and there is a paper relating to errors in analysis of counting statistics (se below), but I had a quick look at this and

[ccp4bb] Re-Release of iMosflm version 7.4.0

2021-09-16 Thread Andrew Leslie - MRC LMB
ast ~2-3 months have been beta versions and should now be replaced with the latest version. Andrew Leslie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?

[ccp4bb] iMosflm version 7.4.0 release withdrawn

2021-09-04 Thread Andrew Leslie - MRC LMB
to the bulletin board when this has been done. Apologies to anyone affected by this, Andrew Leslie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB

[ccp4bb] New iMosflm release, version 7.4.0

2021-09-02 Thread Andrew Leslie - MRC LMB
placed with the latest version. Andrew Leslie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

2021-08-30 Thread Andrew Leslie - MRC LMB
Dear Kay and Jon, I cannot remember Ian Tickles original posting on this (assuming that it was made to the bulletin board), but surely the resolution of the data is also a very important factor in the danger of over-fitting. The lower the resolution, the worse the experimental data to refined

Re: [ccp4bb] How to process two datasets 45 degrees apart?

2021-07-01 Thread Andrew Leslie - MRC LMB
Dear Murpholino, Assuming that the two datasets are from the same crystal, and collected without moving the crystal in-between, then when processing with mosflm I recommend processing both sweeps in the same mosflm run. This is because you will get more accurate

Re: [ccp4bb] Ice ring data issue

2021-03-06 Thread Andrew Leslie
Apologies if this is a duplicate, not clear if the Email I sent 5 hours ago actually got sent. Hi Alex, Although there is an “ice” icon in the imosflm GUI, which excludes all resolution bins where ice ringss are possible, this is not the best way to deal with this. Instead, use

Re: [ccp4bb] Ice ring data issue

2021-03-06 Thread Andrew Leslie
Hi Alex, Although there is an “ice” icon in the imosflm GUI, which excludes all resolution bins where ice ringss are possible, this is not the best way to deal with this. Instead, use the Settings -> Processing options -> Processing tab, where you can specify individual resolution

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

2020-07-23 Thread Andrew Leslie
Dear Reza, I would back Jon’s idea of looking at homologues, although this does depend on how close the homologue is. For example, if your protein has a “P” loop, with the Walker A sequence motif, then I think it would be very surprising if the nucleotide bound in different

Re: [ccp4bb] How many microfocus beamlines are in the world?

2020-06-27 Thread Andrew Leslie
across the world, > detector history and contact details, and for facility people the deposition > statistics pages are an incredibly useful tool for many reasons. > > Best wishes > > Dave > > On 27/06/2020, 12:11, "CCP4 bulletin board on behalf of Andrew Leslie"

Re: [ccp4bb] How many microfocus beamlines are in the world?

2020-06-27 Thread Andrew Leslie
gt; > "Next proposal submission period Mid 2013" > > Not 100% up to date, then. > > Yours, > Rasmus > > On 25/06/2020 09:36, Andrew Leslie wrote: >> Dear Morpholino, >> I think 10 microns or under is a reasonable way to define a micro focus beam >

Re: [ccp4bb] How many microfocus beamlines are in the world?

2020-06-25 Thread Andrew Leslie
Dear Morpholino, I think 10 microns or under is a reasonable way to define a micro focus beam line. There is a list of all MX beamlines at the following web site: http://biosync.rcsb.org/index.jsp This gives details of each beam line, including beam size,

Re: [ccp4bb] Overrefinement considerations and Refmac5.

2020-03-06 Thread Andrew Leslie
I would like to add a small caveat to Eleanor’s rule about a 3% difference being too low for a structure refined against 3Å data. If the 3Å data is for a structure that has already been solved at much higher resolution (e.g. 2Å) and the only difference for the 3Å dataset is a different ligand

Re: [ccp4bb] problems loading images in iMosflm under CCP4

2020-02-12 Thread Andrew Leslie
Dear Annette, Which version of iMosflm are you using? Version 7.2.2, that is currently distributed with the CCP4 suite, will not read Rigaku style Pilatus images (RIPI) correctly, you need version 7.3.0 that can be downloaded from the imosflm website:

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

2020-02-05 Thread Andrew Leslie
important to realise the practical difficulties that organisers face and the considerable effort that is involved in running these workshops. Regards, Andrew Leslie > On 5 Feb 2020, at 00:30, Alejandro Buschiazzo wrote: > > Dear colleagues, > > We are pleased to announce the 8th

Re: [ccp4bb] Dates for the CCP4 Study Weekend on Refinement in 1980

2019-08-24 Thread Andrew Leslie
he Daresbury Study Weekend. I found this information on this > link: http://www.ccp4.ac.uk/html/sfall.html > <http://www.ccp4.ac.uk/html/sfall.html>. > > Regards, > Abhi > > On Sat, Aug 24, 2019 at 7:59 PM Andrew Leslie <mailto:and...@mrc-lmb.cam.ac.uk>> wrot

[ccp4bb] Dates for the CCP4 Study Weekend on Refinement in 1980

2019-08-24 Thread Andrew Leslie
An unusual request perhaps, but does anybody know the actual dates for the 1980 CCP4 Study Weekend on Refinement? I’m hoping that someone keeps better records than me (or is more proficient at using Google)! Thanks, Andrew

[ccp4bb] New release of iMosflm (version 7.3.0)

2019-08-22 Thread Andrew Leslie
the header information, there may be issues with reading the metadata (phi values, detector distance, wavelength etc) from files produced elsewhere, please let me know if this is the case. This latest version will be released as part of the CCP4 package in due course. An

Re: [ccp4bb] Error in data reduction!

2019-07-11 Thread Andrew Leslie
t not able to find the reasons...I >> checked...Disk space is free and have permission to write also. I could able >> to run Pointless, but not Aimless. >> >> Any other reason?? >> >> Thanks >> >> Mike >> >> On Wed, Jul 10, 2019 at 5:37 PM A

Re: [ccp4bb] Error in data reduction!

2019-07-10 Thread Andrew Leslie
I think Helen’s answer is absolutely right. I asked Phil Evans about this when I saw him yesterday, and he said that error usually arises when it is not possible to write the xml file, either because a disk is full, or because you do not have permission to write to that area. Andrew > On 3

[ccp4bb] X-ray equipment available

2018-12-10 Thread Andrew Leslie
We have a Rigaku Actor robot and a HTC Image plate detector that we no longer require. Both are ten years old. If anyone is interested in acquiring these for a nominal sum (plus shipping costs) please let me know. Andrew Leslie MRC LMB, Cambridge

Re: [ccp4bb] Off topic: 'Difficult' Datasets for Processing Practice

2018-09-27 Thread Andrew Leslie
Dear Matthew, I am also late in responding to this, but as part of a Nature Protocols paper on iMosflm (Supplementary Information for Nature Protocols 12, 1310-1325, 2017) I provided a number of examples of “problem datasets”. Some of these are just two images, to show

Re: [ccp4bb] [EXTERNAL] Re: identifying bound ions

2018-08-02 Thread Andrew Leslie
Hi Herman, We can run it stand alone, (i.e. "which xpand” points to an exe that runs) but we have the Uppsala suite installed on our machine. Cheers, Andrew > On 2 Aug 2018, at 07:38, herman.schreu...@sanofi.com wrote: > > Dear Kay, > > I have looked at XPAND and it looks

Re: [ccp4bb] Resolution mismatch aimless/refmac

2018-03-18 Thread Andrew Leslie
Hi Orru, If you have used the normal CCP4 processing pipeline, the data from AIMLESS will go into the “uniqueifyy” script that adds all possible reflections to the MTZ file (down to the lowest possible resolution for your unit cell dimensions), so that might explain why the low

[ccp4bb] New release of iMosflm (7.2.2)

2018-03-12 Thread Andrew Leslie
ll cbf” image format produced on beam lines IO4 and IO3 (and other beamlines in the near future) at the Diamond Light Source. Please notify mos...@mrc-lmb.cam.ac.uk <mailto:mos...@mrc-lmb.cam.ac.uk> of any issues with this version. Andrew Leslie & Harry Powell Allow reading new-style

Re: [ccp4bb] double cell dimensions between P2 and C2

2017-11-09 Thread Andrew Leslie
Dear Markus, I have seen something similar before, I think it was only one cell dimension that was changing (and not the lattice type), but it could double or triple the cell edge, crystals grown in very similar conditions, impossible to tell from morphology what the cell

Re: [ccp4bb] doubt regarding MR search model

2017-09-18 Thread Andrew Leslie
Regarding the warning message "The top solution from a TF rescoring did not pack”, I get this on all the PHASER jobs that I have run recently, but looking through the PHASER log file I cannot see any evidence for packing failure. It may be that the failure is buried in an obscure place in the

Re: [ccp4bb] "reset" a structure before re-refinement

2017-08-17 Thread Andrew Leslie
Hi Graeme, You can do this with PDBSET, keyword NOISE Cheers, Andrew > On 17 Aug 2017, at 16:17, Graeme Winter wrote: > > Dear All, > > Is there a protocol out there to gently perturb atomic positions so that > re-running refinement can essentially put them

Re: [ccp4bb] Indexing question

2017-07-18 Thread Andrew Leslie
I tell POINTLESS to keep C2? > > Grace > > > Grace Beggs > Brennan lab > Department of Biochemistry | Duke University > Email: grace.be...@duke.edu <mailto:grace.be...@duke.edu> > > > From: Andrew Le

Re: [ccp4bb] Rmergicide Through Programming

2017-07-05 Thread Andrew Leslie
I would like to support Graeme in his wish to retain Rmerge in Table 1, essentially for exactly the same reasons. I also strongly support Francis Reyes comment about the usefulness of Rmerge at low resolution, and I would add to his list that it can also, in some circumstances, be more

Re: [ccp4bb] peroxy-glutamate?

2017-05-04 Thread Andrew Leslie
Dear Ed, I find your electron density quite interesting, because generally (I think, I would be happy to be corrected on this) when de-carboxylation of Asp/Glu occurs due to radiation damage, there is no evidence of what happens to the resulting CO2 group. One interpretation of

Re: [ccp4bb] large number in ASU

2017-04-27 Thread Andrew Leslie
Dear Jademilson, At a CCP4 APS workshop a few years ago, one of the students solved a molecular replacement problem where I think there were close to 40 copies in the asu. I have to say that many people were surprised by this, but I think the protein was smaller and

Re: [ccp4bb] Why aren't green reflections on Mosflm integrated?

2016-12-14 Thread Andrew Leslie
Dear Walt, As Tim has said, this is indeed related to the Lorentz correction. These reflections have a large Lorentz correction which is also very sensitive to the crystal orientation, so any small error in orientation can result in a big change to the Lorentz correction and

Re: [ccp4bb] mtz format problem from iMosflm

2015-05-30 Thread Andrew Leslie
Dear Tom, I believe that I once had a similar problem and if I remember correctly (and I'm not certain about this) it was caused by having an extremely large negative intensity (rather than +ve), which could be why the scaling steps did not work because they might only look at +ve values, not

[ccp4bb] Two Postdoctoral Scientist positions at MRC LMB Cambridge

2015-05-06 Thread Andrew Leslie
Posted on behalf of Chris Tate: Postdoctoral Scientist x 2 Structural biology of ion channels by cryo-EM Starting Salary £27,084 – £32,324 Band Salary £27,084 – £39,873 MRC Laboratory of Molecular Biology Two Pfizer-funded Investigator Scientist or Postdoctoral Scientist positions are

[ccp4bb] Reading coords and maps in COOT for PDB entries in mmcif format

2015-04-28 Thread Andrew Leslie
I am trying to get coordinates and maps into COOT for a PDB entry that is only in mmcif format. If I select any of the Fetch PDB … options in COOT, I get the following error message: DEBUG:: in get-url-str: 4wz7 http://www.ebi.ac.uk/pdbe-srv/view/files/4wz7.ent; pdb

Re: [ccp4bb] Thin plate crystals

2015-04-24 Thread Andrew Leslie
There have been quite a few reports that the addition of a low concentration of alcohol (e.g. isopropanol, a few %) can help to increase the thickness of thin plate crystals like these. However, these are probably in the Hampton additive screen that David Briggs suggested. Good luck, Andrew

Re: [ccp4bb] Absence of contact between layers in a crystal

2015-02-06 Thread Andrew Leslie
Just to give a concrete example of Randy's point, PDB entry 2ts1 for tyrosyl tRNA synthetase has layers of molecules with no contact between the layers. This is because the domain (residues 320-419) that was providing the contacts in this direction was disordered and could not be modelled

Re: [ccp4bb] X-ray Source Differences (WAS: RE: [ccp4bb] How far does rad dam travel?)

2015-01-13 Thread Andrew Leslie
Hi Tim, Jacob, I must admit that I was very surprised by the suggestion of a top-hat profile for a in-house rotating anode. We have a Rigaku Fr-E generator, and Rigaku provided a plot of the beam profile for that (with VariMax-HR Optic) and it is very far from being

[ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

2014-09-15 Thread Andrew Leslie
Does anyone know if Molprobity has recently changed the standard bond lengths and angles that it uses ? Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond angle (deviations of 8-10 sigma) for AMPPNP (monomer code ANP) for a new structure refined with Refmac. I then

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

2014-09-15 Thread Andrew Leslie
h.t.jenk...@me.com wrote: On 15 Sep 2014, at 15:24, Andrew Leslie and...@mrc-lmb.cam.ac.uk wrote: This would suggest that the standard dictionary that Molprobity uses has changed, but I cannot find any reference to this on the Molprobity pages. I would

Re: [ccp4bb] ATP library file in REFMAC

2014-08-27 Thread Andrew Leslie
Hi Bernie, This is an issue that the REFMAC developers and the PDB are aware of (at least at the EBI site) and that we have also encountered in a recent deposition. The problem is that there is indeed a discrepancy between the stereochemistry for ATP and ADP as defined in

Re: [ccp4bb] Rename chain ID of water molecules

2014-07-03 Thread Andrew Leslie
Dear Wehne, Have you looked at the CCP4 program watertidy … I think it does what you want (but I have not used it myself). Andrew On 3 Jul 2014, at 04:42, Wenhe wenhezhong.xmu@gmail.com wrote: Dear CCP4BB members, I want to keep the chain ID of water molecules the same as their

Re: [ccp4bb] Helix alignment and movement

2014-05-13 Thread Andrew Leslie
Dear Mike, I think that the old CCP4 superpose program used to be able to do this ? (This was a FORTRAN program, based on code from Wayne Hendrickson's PROLSQ program). With this program you specify one set of residues to do the alignment with and another set to do the

Re: [ccp4bb] metals disapear

2014-05-01 Thread Andrew Leslie
Dear All, So there has been quite a bit of advice on minimising radiation damage, and on some of the effects of radiation damage, but unless I have missed it no-one has come up with a clear cut case where radiation damage actually resulted in the (complete ?) loss of a metal

Re: [ccp4bb] metals disapear - sidetrack - helical scans

2014-05-01 Thread Andrew Leslie
I would just like to back up Ruslan's comments. We have certainly found helical scans to be very valuable at the ESRF and Diamond in minimising radiation damage particularly in cases there the crystal is elongated approximately along the rotation axis direction and where there is not full

Re: [ccp4bb] metals disapear

2014-04-30 Thread Andrew Leslie
Can the radiation damage gurus comment on this ? I know there is a problem with radiation damage changing the valence state of metals, but I don't remember hearing about the metal actually being lost due to radiation damage. Is this really common ? Thanks, Andrew On 30 Apr 2014, at 11:46,

Re: [ccp4bb] twinning problem ?

2014-03-12 Thread Andrew Leslie
Dear Stephen, I have seen a similar effect in the structure of F1-ATPase complexed with the full length inhibitor protein. The inhibitor is a dimer, and it actually couples 2 copies of the ATPase, but it crystallised with only one copy of the ATPase per asymmetric unit.

Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...

2014-02-28 Thread Andrew Leslie
Dear Jacob, Citrate synthase is another early (historically) case, and GAPDH (on binding NAD). Andrew On 27 Feb 2014, at 19:43, Keller, Jacob kell...@janelia.hhmi.org wrote: Dear Crystallographers, Does anyone know of good examples of large, reversible conformational changes occurring

Re: [ccp4bb] Examples of multiple ASU copies with different conformations

2014-01-28 Thread Andrew Leslie
and shows a (physiologically relevant) phosphate binding site that is not found in the other two copies. I would not describe the differences as dramatic though. The paper is: Kabaleeswaran et al., EMBO J 25, 5433 (2006) PDB ID 2HLD Best wishes, Andrew Leslie On 27 Jan 2014, at 18:08, Shane Caldwell

Re: [ccp4bb] Observed criterion sigma(I|F)

2013-11-25 Thread Andrew Leslie
Hi Graeme, There was a CCP4BB thread about this quite recently (14th Nov 2013). I've coped below responses from Edward Berry and Matthew Franklin. SCALA AIMLESS have no sigma cutoffs, but TRUNCATE does. According to the documentation, reflections with intensities less than minus 4 standard

Re: [ccp4bb] Fix cell dimensions

2013-11-18 Thread Andrew Leslie
Dear Niu, It depends on which part of processing you are referring to, i.e. the indexing step or the integration step. In MOSFLM there is no way to enforce cell dimensions during indexing, but providing there is an indexing solution that has cell dimensions close to the ones

Re: [ccp4bb] Fix cell dimensions

2013-11-18 Thread Andrew Leslie
specify it in XDS script. So I wonder is there any way to force this work to be done. Thanks! Best, Niu On Mon, Nov 18, 2013 at 4:56 PM, Andrew Leslie and...@mrc-lmb.cam.ac.uk wrote: Dear Niu, It depends on which part of processing you are referring to, i.e

Re: [ccp4bb] TLS group assignment near poorly ordered loop

2013-08-22 Thread Andrew Leslie
Hi Robbie, I was interested in a couple of things in your response: 1. Slightly different boundaries giving surprisingly different results. Doesn't this suggest that the system is too poorly determined to justify using TLS (and there is the issue that Ethan Merritt has raised

Re: [ccp4bb] mmCIF as working format?

2013-08-05 Thread Andrew Leslie
Hi Tim, I just downloaded GroEL entry 4KI8 in pdb format and cid format from RSCB. The PDB format was 4.7Mb and the CIF format was 5.9Mb, doesn't seem such a big difference to me ? Which example were you looking at ? Andrew On 5 Aug 2013, at 09:03, Tim Gruene

Re: [ccp4bb] delete reflections with negative peak profile correlation

2013-07-31 Thread Andrew Leslie
Dear Rain, I will let XDS expert users provide the definitive response to this because I'm not certain what exactly a negative peak profile correlation indicates. However, I would be very cautious about deleting reflections simply to improve the reported statistics. Taken to

Re: [ccp4bb] Split Crystal Dataprocessing

2013-07-03 Thread Andrew Leslie
It turns out that these images contain two distinct lattices, separated by a rotation of about 5 degrees. Using the development version of iMosflm the two lattices can be easily indexed and integrated. However, the data is quite incomplete due to severe radiation damage. Andrew On 2 Jul

Re: [ccp4bb] ctruncate bug?

2013-06-20 Thread Andrew Leslie
The integration programs report a negative intensity simply because that is the observation. Because of noise in the Xray background, in a large sample of intensity estimates for reflections whose true intensity is very very small one will inevitably get some measurements that are negative.

Re: [ccp4bb] Concerns about statistics

2013-06-14 Thread Andrew Leslie
Hi Boaz, The improvement you see in the cofactor geometry after inclusion of higher resolution data is very interesting, but is it possible that this is a secondary effect resulting from the additional Xray data changing the relative weighting of the Xray and stereochemical terms in the

Re: [ccp4bb] why not read mmcif cell if rpesent?

2013-05-16 Thread A Leslie
Hi Bernhard, When I have used the convert program via ccp4i, the cell and symmetry have indeed been read from the mmcif file and written to the MTZ file. Andrew On 16 May 2013, at 13:50, Bernhard Rupp wrote: Dear Developers, I wonder if there is any particular reason why, if present

Re: [ccp4bb] why not read mmcif cell if rpesent?

2013-05-16 Thread A Leslie
, but the GUI does not populate the corresponding fields. Normally I thought an orange highlighted field is a mandatory field that needs some data… Windows ccp4 6.3.0-020 updated Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of A Leslie Sent: Thursday, May 16

Re: [ccp4bb] vitrification vs freezing

2012-11-15 Thread A Leslie
Dear Sebastiano, This is not entirely straight-forward. The Oxford English dictionary gives the first definition of freeze relevant to this discussion as: Of (a body of) water: be converted into or become covered with ice through loss of heat This is

Re: [ccp4bb] Indexing with XDS

2012-10-09 Thread A Leslie
to ~3.4-3.5Å and then using the merging or refinement statistics to decide the true resolution of the data. Best wishes, Andrew Leslie On 8 Oct 2012, at 23:36, Theresa Hsu wrote: Dear all I took some images from test crystal and tried to index them to get cell parameters, not enough

Re: [ccp4bb] imosflm background definition

2012-09-17 Thread A Leslie
Hi Andreas, The simple answer to this is that you do NOT attempt to redefine the background. Providing the additional spots shown in your image belong to the same lattice, mosflm will automatically exclude pixels from adjacent spots when doing the background plane

Re: [ccp4bb] Aimless and Pointless

2012-09-13 Thread A Leslie
It is possible to force Pointless to select a particular solution, using the Find or match Laue group option in CCP4i. The default option here is Determine Laue group but if you select the Choose a previous solution checkbox you can specify the solution you want Pointless to select, by

[ccp4bb] Problem with indexing in the latest iMosflm release

2012-04-30 Thread A Leslie
is not affected by this error. Apologies to all those that have downloaded this new version. A bug release, that corrects this problem, will be available soon. Thanks to Frank von Delft for bringing this to our attention, mea culpa. Andrew Leslie inline: indexing_solution_failure.tiff

Re: [ccp4bb] unique reflections vs unique observations

2012-04-15 Thread Andrew Leslie
clarify things a bit. Best wishes, Andrew Leslie Dear CCP4 users, I am a bit confused about the use of these terms in regards to structure refinement statistics. When I process my data with SCALA, the program outputs statistics in terms of total and unique numbers of observations

Re: [ccp4bb] Defining beamstop and error during indexing- moslfm

2012-03-22 Thread Andrew Leslie
Dear Sonali, Just to add to Tim's reply, when you open the image with iMosflm, you can Drag and drop the direct beam position in the image display window. First, you have to click on the leftmost icon in the row of icons under the image filename (a green cross) which will display the

Re: [ccp4bb] Defining beamstop and error during indexing- moslfm

2012-03-22 Thread Andrew Leslie
of reflections.So, any suggestions to correct it or am i doing something wrong. Thanks again for the help and suggestions -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” --- On Thu, 22/3/12, Andrew Leslie and...@mrc-lmb.cam.ac.uk wrote: From: Andrew

Re: [ccp4bb] scala and postref

2012-02-22 Thread A Leslie
Hi Vijay, The obvious person to answer this is Phil Evans, but he is in New Zealand at the moment and may well not be reading Emails, so you might need to wait until he is back in the UK (1-2 weeks). I know that he felt the POSTREF option was not an important one to maintain,

Re: [ccp4bb] choice of wavelength

2012-02-16 Thread A Leslie
On 15 Feb 2012, at 23:55, Bart Hazes wrote: Diffracted intensity goes up by the cube of the wavelength, but so does absorption and I don't know exactly about radiation damage. One interesting point is that on image plate and CCD detectors the signal is also proportional to photon energy,

Re: [ccp4bb] (i)mosflm indexing / cell refinement

2011-03-18 Thread A Leslie
Dear Bryan, As Mark van Raaij pointed out you have complete flexibility in specifying the images to be used in autoindexing or in cell refinement. However, the default behaviour is to use the first image and a second image that is as close as possible to 90 degrees away

[ccp4bb] Generating a PDB file for a known ligand

2011-03-15 Thread A Leslie
Dear All, I simply want to create a PDB file for adenosine from the existing monomer library entry ADN.cif. Normally I do this using COOT (get monomer) but when I try this I get the following error: : _lib_update 12/05/10 : -- : ERROR: number of monomers

Re: [ccp4bb] Generating a PDB file for a known ligand

2011-03-15 Thread A Leslie
. I don't understand why these differ (unless Phil change the ADN.cif entry here for some reason). I think we need a comment for the library people ! Cheers Andrew On 15 Mar 2011, at 14:23, Ian Clifton wrote: On 15/03/11 12:57, A Leslie wrote: … I then try using LIBCHECK standalone

Re: [ccp4bb] MOSFILM

2011-03-13 Thread Andrew Leslie
then. For ease of use, we would also strongly recommend using the new mosflm interface (iMosflm) which can be downloaded from the same site. Best wishes, Andrew Leslie Is MOSFILM 6.2.6 the latest version?   Rex Palmer Birkbeck College

Re: [ccp4bb] mosflm gain

2011-03-13 Thread Andrew Leslie
I am fairly certain the article would do nothing to improve the impact factor of the journal in which it was published, but this anecdote might perhaps be useful to Andrew, Phil, and a few other readers of this list. -James Holton MAD Scientist On 3/7/2011 2:00 AM, A Leslie wrote: I

Re: [ccp4bb] mosflm gain

2011-03-07 Thread A Leslie
I have to say that I don't fully agree with James' recommendation to adjust the GAIN in MOSFLM until the calculated SDFAC parameter in SCALA is 1.0. (Background information, the sigmas from Mosflm sd(I) are corrected in SCALA according to sd(I) corrected = SdFac * sqrt{sd(I)**2 +

Re: [ccp4bb] mosflm gain

2011-03-04 Thread A Leslie
Dear Bryan, The quick answer is no. As David Waterman mentioned, it has a default value for the gain for each type of detector that it can deal with. A more detailed answer. An incorrect value for the gain can be indicated by values of the BGRATIO which differ

Re: [ccp4bb] mosflm gain

2011-03-04 Thread A Leslie
Dear All, spotted a mistake in my response, please see the correction below (in bold): There are a host of caveats in this procedure. For example, if the images contains significant diffuse scatter around the Bragg spots, the BGRATIO may be above 1.0 ... this is probably the commonest

[ccp4bb] X-ray facility Scientist at MRC LMB, Cambridge, UK

2011-02-18 Thread A Leslie
X-Ray Facility Scientist MRC Laboratory of Molecular Biology Cambridge £26,022 – £31,758 We wish to recruit an Investigator Scientist to join the MRC Laboratory of Molecular Biology X-ray facility in Cambridge, UK. You will provide support for a range of projects involving X-ray

Re: [ccp4bb] How do I set up a Refmac5 dictionary to constrain octahedrally coordinated Ca++

2010-09-10 Thread A Leslie
Hi Pietro, There are monomer library entries for Ca in various states of coordination by water, entries, OC1, OC2,OC3 etc but unfortunately these are incomplete (no distances or angles with sd's), at least in our CCP4 installation. The entry for octahedral MG-O6, file MO6, is complete

Re: [ccp4bb] non-symmetric tetramer ?

2010-07-29 Thread A Leslie
Hi Fred, If your tetramer show negative cooperativity between the 4 sites for ligand binding, then it is possible to get a tetramer with (say) only one subunit occupied by ligand, which can introduce considerable asymmetry if ligand binding gives rise to a hinge type closure of

Re: [ccp4bb] How to orient molecules in pymol according to the crystal orientation during data collection?

2010-07-07 Thread A Leslie
Dear Anja, I'm not sure why you want the orientation of the molecule in pymol, but working out the orientation of the crystal at phi=0 is straightforward in imosflm. Read the image, index it and go to Strategy. In the strategy pane it gives the angles between the a,b,c

Re: [ccp4bb] How to see miller indeces onto images

2010-06-25 Thread Andrew Leslie
Dear Marco, I'm not sure exactly what you want (for example do you want the indices of ALL reflections to be shown or just individual ones) but iMosflm (CCP4 package) may be able to do what you want. After indexing the image, the predicted reflections will be displayed (as boxes). If

[ccp4bb] LAST CHANCE TO REGISTER FOR DIFFRACTION METHODS GRC

2010-06-21 Thread A Leslie
. = Further details, including a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010program=diffrac We hope to see you there ! Andrew Leslie (Chair) Ana Gonzalez (Vice Chair) Outline Program Diffraction Methods in Structural Biology

[ccp4bb] Diffraction Methods GRC, Registration deadline is 27th June

2010-06-12 Thread Andrew Leslie
a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010program=diffrac We hope to see you there ! Andrew Leslie (Chair) Ana Gonzalez (Vice Chair) Outline Program Diffraction Methods in Structural Biology, 18-23rd July 2010, Bates

Re: [ccp4bb] Scaling question

2010-06-07 Thread A Leslie
Dear Simon, mosflm does indeed estimate the intensity of overloaded reflections, and these are rejected by default in SCALA, but you can choose to include them using the appropriate keywords (ACCEPT OVERLOADS). The number of overloads in the MTZ file, and the number

[ccp4bb] Gordon Conference on Diffraction Methods

2010-05-14 Thread A Leslie
discussions. Further details, including a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010program=diffrac We hope to see you there ! Andrew Leslie (Chair) Ana Gonzalez (Vice Chair) Outline Program: Sunday pm

Re: [ccp4bb] Entering mosflm keywords in imosflm 1.0.4

2010-04-16 Thread A Leslie
The required keystrokes are described (although somewhat hidden) under the heading What's new in version 1.0.0 in the imosflm web page. (www.mrc-lmb.cam.ac.uk/harry/imosflm/ver104) . There are good reasons for this option not being well advertised. One is that if keywords entered in this

[ccp4bb] Gordon Research Conference on Diffraction Methods

2010-04-15 Thread A Leslie
on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010program=diffrac We hope to see you there ! Andrew Leslie (Chair) Ana Gonzalez (Vice Chair) Outline Program: Sunday pm: Macromolecular Structures, Pushing the boundaries Discussion leader: Michael

[ccp4bb] Scientific programmer to work on iMosflm at MRC LMB, Cambridge UK

2010-02-04 Thread A Leslie
. For informal enquiries please contact Andrew Leslie and...@mrc-lmb.cam.ac.uk Your salary will be supported by a flexible pay and reward policy, 30 days annual leave entitlement, an optional MRC final salary pension scheme and excellent on-site sports and social facilities. This position

Re: [ccp4bb] setting cell/spacegroup in imosflm

2009-12-08 Thread A Leslie
Dear Clemens, Yes, this should be possible. If you click on the Cell or Spacegroup line in the Images pane, and then click on the current value, the field becomes editable and you can type in your new values. Best wishes, Andrew On 8 Dec 2009, at 17:41, Clemens Grimm wrote: Dear all,

[ccp4bb] Scientific programmer position at MRC LMB Cambridge UK

2009-11-20 Thread A Leslie
Scientific Programmer MRC Laboratory of Molecular Biology Cambridge £20,074 – £27,271 per annum A two year position is available for a programmer to continue the development of a new Graphical User Interface for a widely used program package to process X-ray diffraction data from crystals of

[ccp4bb] X-ray facility scientist at MRC LMB Cambridge, UK

2009-11-20 Thread A Leslie
X-Ray Facility Scientist MRC Laboratory of Molecular Biology Cambridge £26,022 - £31,758 per annum We wish to recruit an Investigator Scientist to join the MRC Laboratory of Molecular Biology X-ray facility in Cambridge, UK. You will provide support for a range of projects involving X-ray

[ccp4bb] NOT: Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

2009-11-17 Thread A Leslie
This discussion seems to have moved a very long way from the original topic, and hence the reported Subject, could this be continued as a new thread please ? Thanks Andrew On 17 Nov 2009, at 11:40, Morten Kjeldgaard wrote: Tim Gruene wrote: Yes, but models that can be validated

[ccp4bb] Nobel prize for chemistry 2009

2009-10-07 Thread A Leslie
BB members may be interested to know that the 2009 Nobel prize for chemistry has been awarded to Venki Ramakrishnan, Tom Steitz and Ada Yonath for their structural work on the bacterial ribosome.

[ccp4bb] Peter Boyd, RIP

2009-09-30 Thread Leslie Kinsland
Posted on behalf of James G. Tobin, LLNL Dear Colleagues, It is with great sorrow that I must report that Peter Boyd has passed away, in his sleep at home on Friday morning, September 25th. His family is planning a private service. If you wish, condolences can be sent to MaryBeth Boyd at

[ccp4bb] Post-doctoral position at the Advanced Photon Source

2009-09-28 Thread Leslie Kinsland
The Northeastern Collaborative Access Team (NE-CAT), located at the Advanced Photon Source at the Argonne National Laboratory near Chicago, is seeking applicants for a Postdoctoral Research Associate position. This is a two year appointment beginning as soon as possible. In addition to

Re: [ccp4bb] Summary for Anisotropic Diffraction In Refinement question

2009-09-16 Thread A Leslie
this option and so cannot compare its efficacy relative to integrating isotropically and then applying an anisotropic limit such as Justin describes. Andrew Leslie On 15 Sep 2009, at 21:48, Justin Hall wrote: Dear All; In response to my Anisotropic Diffraction In Refinement, which asked

Re: [ccp4bb] imosflm with multiple data sets

2009-08-18 Thread Andrew Leslie
on separate sub-nodes.) Andrew Leslie wrote: Dear Tom, There is a straightforward way to do what you want. It is probably simplest to start by reading in only the images from the first segment (0-180). Then do the indexing, cell refinement and integration in the usual way

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